Marine Sediments Illuminate Chlamydiae Diversity and Evolution

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Prokaryotic diversity in Zostera noltii-colonized marine sediments

The diversity of microorganisms present in a sediment colonized by the phanerogam Zostera noltii has been analyzed. Microbial DNA was extracted and used for constructing two 16S rDNA clone libraries for Bacteria and Archaea. Bacterial diversity was very high in these samples, since 57 different sequences were found among the 60 clones analyzed. Eight major lineages of the Domain Bacteria were represented in the library. The most frequently retrieved bacterial group (36% of the clones) was delta-Proteobacteria related to sulfate-reducing bacteria. The second most abundant group (27%) was gamma-Proteobacteria, including five clones closely related to S-oxidizing endosymbionts. The archaeal clone library included members of Crenarchaeota and Euryarchaeota, with nine different sequences among the 15 analyzed clones, indicating less diversity when compared to the Bacteria organisms. None of these sequences was closely related to cultured Archaea organisms.     

Diversity of Thiosulfate-Oxidizing Bacteria from Marine Sediments and Hydrothermal Vents

Species diversity, phylogenetic affiliations, and environmental occurrence patterns of thiosulfate-oxidizing marine bacteria were investigated by using new isolates from serially diluted continental slope and deep-sea abyssal plain sediments collected off the coast of New England and strains cultured previously from Galapagos hydrothermal vent samples. The most frequently obtained new isolates, mostly from 10³- and 10⁴-fold dilutions of the continental slope sediment, oxidized thiosulfate to sulfate and fell into a distinct phylogenetic cluster of marine alpha-Proteobacteria. Phylogenetically and physiologically, these sediment strains resembled the sulfate-producing thiosulfate oxidizers from the Galapagos hydrothermal vents while showing habitat-related differences in growth temperature, rate and extent of thiosulfate utilization, and carbon substrate patterns. The abyssal deep-sea sediments yielded predominantly base-producing thiosulfate-oxidizing isolates related to Antarctic marine Psychroflexus species and other cold-water marine strains of the Cytophaga-Flavobacterium-Bacteroides phylum, in addition to gamma-proteobacterial isolates of the genera Pseudoalteromonas and Halomonas-Deleya. Bacterial thiosulfate oxidation is found in a wide phylogenetic spectrum of Flavobacteria and Proteobacteria.     

Culture-Dependent and Independent Studies of Microbial Diversity in Highly Copper-Contaminated Chilean Marine Sediments

Cultivation and molecular-based approaches were used to study microbial diversity in two Chilean marine sediments contaminated with high (835 ppm) and very high concentrations of copper (1,533 ppm). The diversity of cultivable bacteria resistant to copper was studied at oxic and anoxic conditions, focusing on sulfate-, thiosulfate-, and iron-reducing bacteria. For both sediments, the cultivable bacteria isolated at oxic conditions were mostly affiliated to the genus Bacillus, while at anoxic conditions the majority of the cultivable bacteria found were closely related to members of the genera Desulfovibrio, Sphingomonas, and Virgibacillus. Copper resistance was between 100 and 400 ppm, with the exception of a strain affiliated to members of the genus Desulfuromonas, which was resistant up to 1,000 ppm of copper. In parallel, cloning and sequencing of 16S rRNA was performed to study the total bacterial diversity in the sediments. A weak correlation was observed between the isolated strains and the 16S rRNA operational taxonomic units detected. The presence of copper resistance genes (copA, cusA, and pcoA) was tested for all the strains isolated; only copA was detected in a few isolates, suggesting that other copper resistance mechanisms could be used by the bacteria in those highly copper-contaminated sediments.     

Diversity of Oligotrichia and Choreotrichia Ciliates in Coastal Marine Sediments and in Overlying Plankton

Elucidating the relationship between ciliate communities in the benthos and the plankton is critical to understanding ciliate diversity in marine systems. Although data for many lineages are sparse, at least some members of the dominant marine ciliate clades Oligotrichia and Choreotrichia can be found in both plankton and benthos, in the latter either as cysts or active forms. In this study, we developed a molecular approach to address the relationship between the diversity of ciliates in the plankton and those of the underlying benthos in the same locations. Samples from plankton and sediments were compared across three sites along the New England coast, and additional subsamples were analyzed to assess reproducibility of methods. We found that sediment and plankton subsamples differed in their robustness to repeated subsampling. Sediment subsamples (i.e., 1-g aliquots from a single ∼20-g sample) gave variable estimates of diversity, while plankton subsamples produced consistent results. These results indicate the need for additional study to determine the spatial scale over which diversity varies in marine sediments. Clustering of phylogenetic types indicates that benthic assemblages of oligotrichs and choreotrichs appear to be more like those from spatially remote benthic communities than the ciliate communities sampled in the water above them.Planktonic ciliates provide a critical trophic link between the microbial and macroscopic components of the pelagic food web, and the subclasses Choreotrichia and Oligotrichia are the most abundant ciliate groups in this environment (46). One key to understanding the diversity and ecology of Choreotrichia and Oligotrichia is the relationship between benthic and planktonic forms. While the ciliates in these two groups are predominantly swimmers (54), there is crossover between benthic and pelagic environments for many species. Some taxa are described as epibenthic, living in the layer of water just above the sediment (16, 54), some have the capacity to live attached to sediment particles for a period and then become free-swimming (21), and a large number of taxa within these two groups spend a portion of their life cycles in dormancy, persisting in the sediments in cyst form (22, 23, 25, 35, 36, 39, 40, 41, 43, 49, 51). An accurate assessment of ciliate dynamics in the plankton requires careful study of both benthic and pelagic environments and the extent of coupling between the two environments.The role of the cyst in the life cycle of marine planktonic ciliates is particularly critical for understanding their distribution, evolutionary history, and ecology (6) as cysts provide a mechanism for dormancy during periods of poor environmental conditions. Relatively few marine ciliate species have been directly studied to determine conditions for encystment and excystment, period of dormancy (22, 23, 25, 26, 43), and role of the encystment cycle in the ecology of the organism (36). Moreover, studies on the conditions related to encystment and excystment in ciliates reveal different patterns and potential causes depending on the species (22, 23, 25, 26, 36, 43). While some data link the cycle of encystment with environmental factors such as light (23), temperature (23, 25, 26), and presence of food (22), other data suggest a temporal/seasonal cycling independent of external environmental conditions (26, 36, 43).A further factor limiting our understanding of the role of cysts in the life cycle of ciliates is identification based on the limited morphological features of the cysts, which are highly convergent (4, 17). In the case of ciliates that encyst within a lorica, as in the tintinnids, this is less of a problem (45), but for aloricate species, identification is not certain without direct observation of excystment (41, 48). Hence, morphological surveys of ciliates in benthic environments frequently capture members of the Oligotrichia and Choreotrichia (19, 31, 52, 53, 54) but are often limited to identification at the genus level using morphological approaches.More is known about planktonic ciliates, where morphology provides a wealth of data (11) and where molecular studies have revealed tremendous diversity, with many rare haplotypes (10). We define distinct sequences at the small-subunit (SSU) ribosomal DNA (rDNA) locus as haplotypes to remain conservative in our approach to identifying operational taxonomic units (OTUs) because ciliates have an unusual genome structure with high chromosome copy number, which potentially could generate multiple sequence types for the same locus within an organism or within a species. Planktonic ciliates show high molecular diversity at the SSU rDNA locus (10, 24), and primer sequences have been developed to detect ciliates from environmental samples within the subclasses Choreotrichia and Oligotrichia (10). Ciliates from these subclasses sampled across three coastal locations comprised distinct assemblages, with a few ubiquitous and abundant haplotypes (10) and many singletons (haplotypes unique to a particular sample).This study lays the groundwork for an alternative to morphological methods for analyzing benthic assemblages of oligotrichs and choreotrichs and comparing them to assemblages in the overlying water. Our goal was to compare levels of genetic diversity between sediment and plankton samples as a means of assessing the potential of methods for monitoring exchange between these two communities. There are two main questions addressed in this study: (i) are the two environments, plankton and sediment, comparable in robustness to repeated sampling using PCR, cloning, and sequencing and (ii) what is the relationship between genetic diversity of oligotrich and choreotrich ciliate communities sampled in marine sediments and in the plankton?To investigate the first question, we designed resampling experiments in plankton and sediment collections to test spatial heterogeneity as well as the robustness of repeated PCR cloning and sequencing for capturing diversity. Using two plankton samples collected by different means from the same time and place, we compared the similarity of subsamples in this environment to the similarity between separate subsamples of sediment collected at the same time and place. Additionally, we resampled DNA extracted from each of the two environments and investigated the reproducibility of repeated PCR cloning and sequencing between environmental types.To investigate the second question, we compared the diversity in sediment samples collected in the Gulf of Maine and Long Island Sound in May 2005 to previously published data from plankton samples collected at the same times and locations (10). Cluster analyses of the communities in sediment and plankton were used to determine the degree of coupling between the benthic and pelagic forms of Oligotrichia and Choreotrichia. The predicted result would be that the ciliate community observed in the plankton represents a subset of the diversity found in the benthic community, including cysts, beneath it. While the community in the plankton for many oligotrichs and choreotrichs would change depending on prevailing environmental conditions, predation, and chance, the benthic community, which includes encysted planktonic forms, should represent the longer-term diversity in a given region.     

Tube-dwelling Meiofauna in Marine Sediments

Tube-dwelling has been recognized previously as a life-style for several meiobenthic species, but behavioural observation of living specimens has rarely been reported. The extent to which tube-building and tube-dwelling occurs within meiofauna, and how they have influenced evolutionary and ecological processes as well as morphology within these organisms, is relatively unknown but potentially of great significance. In addition to direct observation of tube-building and the occurence of tubes in natural habitats, the internal anatomy associated with tube-building in two nematode species (Ptycholaimellus jacobi, P. ponticus) and one harpacticoid copepod species (Stenhelia palustris) is the focus of this study. Special attention is given to the secretory products, glands, and their association with secretory pores. Also, the role of meiobenthic tube-dwelling activities in relationship to their environment is extensive discussed.     

Microbial Diversity in the Deep Marine Sediments from the Qiongdongnan Basin in South China Sea

The continental shelf and slope in the northern South China Sea is well known for its prospect of oil/gas/gas-hydrate resources. To study microbial communities and their roles in carbon cycling, a 4.9-m sediment core was collected from the Qiongdongnan Basin on the continental slope of the South China Sea during our cruise HY4-2005-5 in 2005. Geochemical, mineralogical, and molecular phylogenetic analyses were carried out. Sulfate concentration in pore water decreased with depth. Abundant authigenic carbonates and pyrite were observed in the sediments. The bacterial community was dominated by aerobic and facultative organisms. Bacterial clone sequences belonged to the Gamma-, Alpha-, Deltaproteobacteria and Firmicutes group, and they were related to Fe(III) and/or Mn(IV) reducers, sulfate reducers, aromatic hydrocarbon degraders, thiosulfate/sulfite oxidizers, and denitrifiers. Archaeal clone sequences exhibited greater overall diversity than the bacterial clones with most sequences related to Deep-Sea Archaeal Group (DSAG), Miscellaneous Crenarchaeotic Group (MCG), and Uncultured Euryarchaeotic Clusters (UECs). Archaeal sequences related to Methanosarcinales, South African Gold Mine Euryarchaeotic Group (SAGMEG), Marine Benthic Group-D (MBG-D) were also present. Most of these groups are commonly present in deep-sea sediments, particularly in methane/organic-rich or putative methane hydrate-bearing sediments.     

Salt-Stimulated Bicarbonate-Dependent Photosynthesis in the Marine Angiosperm Zostera muelleri

Millhouse, J. and Strother, S. 1986. Salt-stimulated bicarbonate-dependentphotosynthesis in the marine angiosperm Zostera muelleri.—J.exp. Bot. 37: 965–976. Photosynthetic oxygen evolution in the seagrass Zostera muelleriIrmisch ex Aschers. was inhibited in iso-osmotic sucrose. Theapparent affinity of the leaves for CO₂ in seawater increasesfrom pH 8?2 to 8?9 indicating that as well as CO₂ may act as a substrate for photosynthesis. Theaffinity for CO₂ was lower in iso-osmotic sucrose and was notaffected by pH. Under these conditions was not a substrate for photosynthesis. The differencebetween the photosynthetic rate in seawater and iso-osmoticsucrose at the same concentration of CO₂ was used to estimate assimilation. The Briggs-Maskell equation, which allows for an unstirred layer around the tissuewas more appropriate than the Michaelis-Menten theory for calculatingthe apparent affinity of the leaf slices for CO₂. The apparentK_m CO₂ was calculated as 116 mmol m^–3 at pH 8?2 by Michaelis-Mentenkinetics but only 8?10 mmol m^–3 by the Briggs-Maskellequation. The stimulation by various ions in Seawater of use was investigated. The cations,in decreasing order of effectiveness were Ca²⁺, Mg²⁺, K⁺ andNa⁺ Anions were ineffective. No single cation at its concentrationin seawater was capable of supporting use at the rate observed in seawater. Acetazolamide,an inhibitor of carbonic anhydrase, inhibited the use of for photosynthesis but had littleeffect on CO₂ photosynthesis. Thus, carbonic anhydrase activityis required for -dependent photosynthesis. Key words: Zostera muelleri, photosynthesis, salinity     

Diversity of Benzylsuccinate Synthase-Like (bssA) Genes in Hydrocarbon-Polluted Marine Sediments Suggests Substrate-Dependent Clustering

The potential of hydrocarbon biodegradation in marine sediments was determined through the detection of a functional biomarker, the bssA gene, coding for benzylsuccinate synthase, the key enzyme of anaerobic toluene degradation. Eight bssA clone libraries (409 sequences) were constructed from polluted sediments affected by the Prestige oil spill in the Atlantic Islands National Park and from hydrocarbon-amended sediment microcosms in Mallorca. The amplified products and database-derived bssA-like sequences grouped into four major clusters, as determined by phylogenetic reconstruction, principal coordinate analysis (PCoA), and a subfamily prediction tool. In addition to the classical bssA sequences that were targeted, we were able to detect sequences homologous to the naphthylmethylsuccinate synthase gene (nmsA) and the alkylsuccinate synthase gene (assA), the bssA homologues for anaerobic 2-methylnaphthalene and alkane degradation, respectively. The detection of bssA-like variants was determined by the persistence and level of pollution in the marine samples. The observed level of gene diversity was lower in the Mallorca sediments, which were dominated by assA-like sequences. In contrast, the Atlantic Islands samples, which were highly contaminated with methylnaphthalene-rich crude oil, showed a high proportion of nmsA-like sequences. Some of the detected genes were phylogenetically related to Deltaproteobacteria communities, previously described as the predominant hydrocarbon degraders at these sites. Differences between all detected bssA-like genes described to date indicate separation between marine and terrestrial sequences and further subgrouping according to taxonomic affiliation. Global analysis suggested that bssA homologues appeared to cluster according to substrate specificity. We observed undetected divergent gene lineages of bssA homologues, which evidence the existence of new degrader groups in these environments.     

Diversity of Prokaryotic Community at a Shallow Marine Hydrothermal Site Elucidated by Illumina Sequencing Technology

To investigate the prokaryotic community structure and composition in an active hydrothermal site, named Black Point, off Panarea Island (Eolian Islands, Italy), we examined sediment and fluid samples, differing in temperature, by a massive parallel sequencing (Illumina) technique targeting the V3 region of the 16S rRNA gene. The used technique enabled us to detect a greater prokaryotic diversity than that until now observed and to reveal also microorganisms occurring at very low abundance (≤0.01 %). Most of sequences were assigned to Bacteria while Archaea were a minor component of the microbial community in both low- and high-temperature samples. Proteobacteria (mainly consisting of Alpha-, Gamma-, and Epsilonproteobacteria) dominated among all samples followed by Actinobacteria and Bacteroidetes. Analyzed DNA obtained from samples taken at different temperatures indicated the presence of members of different dominant genera. The main differences were observed between sediment samples where Rhodovulum and Thiohalospira prevailed at high temperature, while Thalassomonas and Sulfurimonas at low temperature. Chlorobium, Acinetobacter, Sulfurimonas, and Brevundimonas were abundant in both low- and high-temperature fluid samples. Euryarchaeota dominated the archaeal community in all samples. Classes of Euryarchaeota embracing hyperthermophilic members (Thermococci and Thermoplasmata) and of Crenarchaeota (Thermoprotei) were more abundant in high-temperature samples. A great number of sequences referred to Bacteria and Archaea still remained unaffiliated, indicating that Black Point site represents a rich source of so-far uncharted prokaryotic diversity.     

Temporal Variations of Microbial Activity and Diversity in Marine Tropical Sediments (New Caledonia Lagoon)

Temporal variations of oxygen consumption, sensitivity to metal spiking, and microbial diversity were investigated during a one-year survey at the sediment–water interface in the tropical lagoon of New Caledonia. Sediment oxygen consumption (SOC) exhibited strong variations with time with maximum rates during February (Austral summer) and minimum values during July (cold period). SOC was strongly positively correlated with temperature, with an apparent activation energy (E _a) of 41 kJ mol⁻¹, corresponding to an apparent Q ₁₀(20–30 °C) of 1.75. Strong short-term variations of SOC were also observed with ratios between two consecutive samplings reaching up to twofold of magnitude within one week, whereas the maximum/minimum ratio over the whole year was equal to 2.73. In most cases, metal spiking led to a strong decrease of SOC; however, in a third of sampling dates, spiking did not significantly decrease activity. These periods of apparent metal tolerance were not characterized by a particular bacterial community structure. Bacterial community structure estimated from terminal restriction fragment length polymorphism (T-RFLP) analysis exhibited strong variations over the one-year survey, and no seasonality was observed for bacterial richness. However, on average, the Whittaker similarity index between two consecutive T-RFLP profiles was above 60% suggesting a relative stability of the bacterial community structure on the short timescale with prominent T-RFs representing on average more than 67% of relative abundance occurring over most of the year, whereas other T-RFs only occurred during some periods.     

The Link between Microbial Diversity and Nitrogen Cycling in Marine Sediments Is Modulated by Macrofaunal Bioturbation

Objectives

The marine benthic nitrogen cycle is affected by both the presence and activity of macrofauna and the diversity of N-cycling microbes. However, integrated research simultaneously investigating macrofauna, microbes and N-cycling is lacking. We investigated spatio-temporal patterns in microbial community composition and diversity, macrofaunal abundance and their sediment reworking activity, and N-cycling in seven subtidal stations in the Southern North Sea.

Spatio-Temporal Patterns of the Microbial Communities

Our results indicated that bacteria (total and β-AOB) showed more spatio-temporal variation than archaea (total and AOA) as sedimentation of organic matter and the subsequent changes in the environment had a stronger impact on their community composition and diversity indices in our study area. However, spatio-temporal patterns of total bacterial and β-AOB communities were different and related to the availability of ammonium for the autotrophic β-AOB. Highest bacterial richness and diversity were observed in June at the timing of the phytoplankton bloom deposition, while richness of β-AOB as well as AOA peaked in September. Total archaeal community showed no temporal variation in diversity indices.

Macrofauna, Microbes and the Benthic N-Cycle

Distance based linear models revealed that, independent from the effect of grain size and the quality and quantity of sediment organic matter, nitrification and N-mineralization were affected by respectively the diversity of metabolically active β-AOB and AOA, and the total bacteria, near the sediment-water interface. Separate models demonstrated a significant and independent effect of macrofaunal activities on community composition and richness of total bacteria, and diversity indices of metabolically active AOA. Diversity of β-AOB was significantly affected by macrofaunal abundance. Our results support the link between microbial biodiversity and ecosystem functioning in marine sediments, and provided broad correlative support for the hypothesis that this relationship is modulated by macrofaunal activity. We hypothesized that the latter effect can be explained by their bioturbating and bio-irrigating activities, increasing the spatial complexity of the biogeochemical environment.     

Biodegradation of Pyrene in Marine Beach Sediments

The potential of chitosan (0.1% dry weight equivalent) as a bioremediation additive for removal of the recalcitrant polycyclic aromatic hydrocarbon (PAH) pyrene in marine beach sediments was investigated using an open irrigation system over a 63-day period. Osmocote, a slow release fertilizer, was used as the key nutrient supplement at a concentration of 1% in sediment (dry weight equivalent). Osmocote significantly (p < .05) enhanced nutrient levels, and the metabolic activity of the indigenous microbial biomass. Both additives were comparable in stimulating pyrene biodegradation rates; with chitosan (0.062 day^?1) being slightly more effective as an amendment than Osmocote (0.051 day^?1). Loss of pyrene in a control sediment (i.e., pyrene, without additives) was 66.6% over a 63-day period. The concurrent application of additives yielded the greatest biodegradation rates (0.072day^?1), resulting in a 98.2% loss of pyrene over 63 days. The treatment of oil contaminated beach sediments with both osmocote (1%) and chitosan (0.1%) is therefore recommended as an effective treatment for the intrinsic biodegradation of recalcitrant PAHs in oil-contaminated beach sediments.     

Determination of Virus Abundance in Marine Sediments

In this study, we optimized procedures to enumerate viruses from marine sediments by epifluorescence microscopy using SYBR Green I as a stain. The highest virus yields from the bulk of the sediments were obtained by utilizing pyrophosphate and 3 min of sonication. The efficiency of extraction benthic viruses by pyrophosphate-ultrasound treatment was about 60% of the extractable virus particles. Samples treated with nucleases had increased virus counts, suggesting a masking effect of extracellular DNA. No significant differences were observed between virus counts obtained by epifluorescence microscopy and transmission electron microscopy. Both formaldehyde and glutaraldehyde gave significant reductions of virus counts after only 24 h of sediment storage, but no further loss occurred after 7 days.     

Characterization of beta-Glucosidase Activity in Intertidal Marine Sediments

Glycoside derivatives of 4-methylumbelliferone (MUF) were used to characterize the polysaccharidase enzyme systems present in sediments from an intertidal mud flat. The formation of highly fluorescent MUF on hydrolysis of the various glycosides was determined at low substrate concentrations (<1 muM) and with short incubation periods (>5 min). The hydrolysis of MUF-beta-d-glucose in sediments from depth intervals of 0 to 2 cm was insensitive to the presence of oxygen, dissolved sulfide, and iron; magnesium and calcium were stimulatory, however. A pronounced temperature optimum was observed at 40 degrees C, a salinity optimum at 30 per thousand, and a pH optimum at 8.5. Rates of hydrolysis were completely inhibited by the addition of mercuric chloride and sodium azide, but only partially inhibited by toluene and the specific beta-glucosidase inhibitor delta-1,5-gluconolactone. The response to delta-1,5-gluconolactone suggested that about 50% of the observed hydrolysis of MUF-beta-d-glucoside was due to exo- and endoglucanases. A wide variety of hydrolytic activities was observed, with at least some nonspecificity occurring in the case of MUF-beta-d-fucoside. Depth profiles indicated maximal activity in surface sediments with a rapid decline below 2 cm. MUF-glycosides provided a convenlent tool for initial analyses of the dynamics and controls of polymer hydrolysis in marine sediments.     

Methane Production in Shallow-Water, Tropical Marine Sediments

The in situ production of methane was monitored in several types of tropical benthic communities. A bed of Thalassia testudinum located in Caesar Creek (Florida Keys) exhibited the highest methanogenic activity (initial rates = 1.81 to 1.86 mumol CH4/m2 per h) as compared with another seagrass (Syringodium sp., 0.15 to 0.33 mumol/m2 per h) and two coral reef environments (Hydro-Lab, 0.016 to 0.10 mumol/m2 per h; Curacao, 0.14 to 0.47 mumol/m2 per h). The results suggest that a wide variety of benthic metabolic processes (e.g., photosynthetic oxygen production) influences methane production rates.     

Prokaryotic Metabolic Activity and Community Structure in Antarctic Continental Shelf Sediments

The prokaryote community activity and structural characteristics within marine sediment sampled across a continental shelf area located off eastern Antarctica (66°S, 143°E; depth range, 709 to 964 m) were studied. Correlations were found between microbial biomass and aminopeptidase and chitinase rates, which were used as proxies for microbial activity. Biomass and activity were maximal within the 0- to 3-cm depth range and declined rapidly with sediment depths below 5 cm. Most-probable-number counting using a dilute carbohydrate-containing medium recovered 1.7 to 3.8% of the sediment total bacterial count, with mostly facultatively anaerobic psychrophiles cultured. The median optimal growth temperature for the sediment isolates was 15°C. Many of the isolates identified belonged to genera characteristic of deep-sea habitats, although most appear to be novel species. Phospholipid fatty acid (PLFA) and isoprenoid glycerol dialkyl glycerol tetraether analyses indicated that the samples contained lipid components typical of marine sediments, with profiles varying little between samples at the same depth; however, significant differences in PLFA profiles were found between depths of 0 to 1 cm and 13 to 15 cm, reflecting the presence of a different microbial community. Denaturing gradient gel electrophoresis (DGGE) analysis of amplified bacterial 16S rRNA genes revealed that between samples and across sediment core depths of 1 to 4 cm, the community structure appeared homogenous; however, principal-component analysis of DGGE patterns revealed that at greater sediment depths, successional shifts in community structure were evident. Sequencing of DGGE bands and rRNA probe hybridization analysis revealed that the major community members belonged to delta proteobacteria, putative sulfide oxidizers of the gamma proteobacteria, Flavobacteria, Planctomycetales, and Archaea. rRNA hybridization analyses also indicated that these groups were present at similar levels in the top layer across the shelf region.